Related papers: On the accuracy of ancestral sequence reconstructi…
In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular,…
Recurrence formulas are presented for studying the accuracy of the Fitch method for reconstructing the ancestral states in a given phylogenetic tree. As their applications, we analyze the convergence of the accuracy of reconstructing the…
In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex $v$ of an evolutionary tree $T$ from the states that are observed at the leaves of the tree. A simple and fast…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…
One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Complex systems of polynomial equations have to be set up and solved algebraically in order to obtain analytic solutions for maximum likelihood on phylogenetic trees. This has restricted the types of systems previously resolved to the…
We consider the problem of inferring an ancestral state from observations at the leaves of a tree, assuming the state evolves along the tree according to a two-state symmetric Markov process. We establish a general branching rate condition…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this paper we propose a topology reconstruction method consistent with the most…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry…
The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies…